I had this also, and tracked it down to the following (along with a solution)
- After installing Ios8 I had enabled family sharing for my kids iPad, changing what was a second existing iPad using my app ID to one of his own under a family sharing (child) arrangement. The effect of this change was that all apps on his device became 'shared' from my owner Apple id (as organiser of the share) at the time I enable the child device under family sharing.
- on my kids iPad, without realising it, one of these shared apps was NOT enabled by the publisher for family sharing. This remained invisible until...
- The application was updated by the publisher ... NOW the update software of the App Store checked the family sharing status, realising the app was not available for family sharing, and voila! ... There is your OP's message coming up during the App Store update attempt.
- SOLUTION: For me, the app was free, and there was no unrecoverable data to worry about, so to solve the problem I just deleted the app from the child iPad, and then did a 'purchase / request / download ' from the same iPad. Now Apple sees it as his, not shared from me. Problem solved. this solution is sub-optimal if you have data attached to the app that you don't want to delete, or if you don't want to pay twice... but it IS up to the publisher - and they may NEVER allow family sharing - you would have to pay twice if you want such an app on multiple devices anyway...
Now to Apple - who does trawl this forum looking for answers - for you I would suggest you verify all apps installed on a device that is entering family sharing arrangements to ensure ALL currently installed apps are enabled for family sharing. If they are NOT, you need to warn and delete or back out of the setup. I suppose you could also offer to download said apps during family setup (at possible additional cost) but I suspect there would be complications around purchased data and the Apple ID that it belonged to ... But whatever works...
hope this helps someone...
TSE